Tools and services tutorials
Version 10.1 by annedevismes on 2023/02/22 14:23
Findable. Accessible. User-facing.
Welcome to the single entry point to tutorials for EBRAINS tools and services. Here, you can find a list of EBRAINS offerings, sorted by topic, and links to their tutorials.
Some tutorials are also available on EBRAINS YouTube channel.
Arbor
- A simple single cell model (beginner)
- A detailed single cell model (advanced)
- A detailed single cell recipe (advanced)
- A ring network (advanced)
- A simple dendrite (advanced)
- A simple single cell recipe (advanced)
- A single cell model from the Allen Brain Atlas (advanced)
- A single cell model from the BluePyOpt Cell Optimisation Library (advanced)
- Distributed ring network (MPI) (advanced)
- Extracellular signals (LFPykit) (advanced)
- GPU and profiling (advanced)
- Spike Timing-dependent Plasticity Curve (advanced)
- Two cells connected via a gap junction (advanced)
Electrophysiology Analysis Toolkit
- Statistics of spike trains (beginner)
- ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains (advanced)
- Gaussian Process Factor Analysis (advanced)
- Parallel (advanced)
- Spike Pattern Detection and Evaluation (SPADE) (advanced)
- The Unitary Events Analysis (advanced)
- Time-domain Granger Causality (advanced)
NEST
- Introduction to NEST: Simulating a single neuron (beginner)
- Neurons and simple neural networks (beginner)
- Populations of neurons (beginner)
- Connect two NEST simulations using MUSIC (advanced)
- Connecting networks with synapses (advanced)
- Introduction to the MUSIC Interface (advanced)
- MUSIC Connections in C++ and Python (advanced)
- MUSIC with SLI (advanced)
- Practical tips (advanced)
- Spatially structured networks (advanced)
- The pymusic interface (advanced)
NESTML
- Izhikevich tutorial (beginner)
- Active dendrite tutorial (advanced)
- Dopamine-modulated STDP synapse tutorial (advanced)
- Ornstein-Uhlenbeck noise tutorial (advanced)
- STDP synapse tutorial (advanced)
- STDP windows tutorial (advanced)
Neuron
- Construction and Use of Models: Part 1. Elementary tools (beginner)
- The hoc programming language (beginner)
- Introduction to Network Construction (advanced)
- 1. Implement and test the computational model itself (advanced)
- 2. Run a "complete" simulation and save its results (advanced)
- 3. Run a segmented simulation and save its results (advanced)
- 3D/Hybrid Intracellular Tutorial (advanced)
- 4. Reconstitute and verify the "complete" simulation results (advanced)
- A NEURON Programming Tutorial - Part A (advanced)
- A NEURON Programming Tutorial - Part B (advanced)
- A NEURON Programming Tutorial - part C (advanced)
- A NEURON Programming Tutorial - Part E (advanced)
- Ball and Stick model part 1 (advanced)
- Ball and Stick model part 2 (advanced)
- Ball and Stick model part 3 (advanced)
- Ball and Stick model part 4 (advanced)
- Creating a channel from a kinetic scheme specification (advanced)
- Creating a channel from an HH-style specification (advanced)
- Creating a model of stochastic channel gating (advanced)
- Creating a stylized ("stick figure") model cell (advanced)
- Dealing with simulations that generate a lot of data (advanced)
- Example: circadian rhythm (advanced)
- Example: restricting a reaction to part of a region (advanced)
- Exploring morphometric data and fixing problems (advanced)
- Extracellular Diffusion (advanced)
- How to generate independent random spike streams (advanced)
- Managing a model cell with complex anatomy (advanced)
- mGluR example (advanced)
- ModelView: Compact display of parameters for NEURON models. (advanced)
- Python introduction (advanced)
- Randomness in NEURON models (advanced)
- Reaction-Diffusion (advanced)
- Reaction-Diffusion: Calcium Wave (advanced)
- Reaction-Diffusion: Thresholds (advanced)
- Reaction-Diffusion: varying initial concentrations and parameters (advanced)
- Reading a morphometric data file and converting it to a NEURON model (advanced)
- RxD with MOD files (advanced)
- Scripting NEURON basics (advanced)
- Segmenting a simulation of a model cell (advanced)
- Segmenting a simulation of a model network (advanced)
- Source code that demonstrates the solution (advanced)
- Specifying parameterized variation of biophysical properties (advanced)
- The solution (advanced)
- Tutorial 1 : Fitting a function to data (advanced)
- Tutorial 1: Making Networks of Artificial Neurons (advanced)
- Tutorial 2 : Fitting a model to data (advanced)
- Tutorial 2: Making Hybrid Nets (advanced)
- Using Import3D (advanced)
- Using NEURON's Optimization Tools (advanced)
Neurorobotics Platform
PyNN
- Building and simulating a simple model (beginner)
- Installing PyNN on a Linux system (beginner)
The Virtual Brain
- Building Your Own Brain Network Model (beginner)
- Getting Started (beginner)
- My first simulation with The Virtual Brain (beginner)
- Population Models in The Virtual Brain (TVB) and the Phase Plane (beginner)
- Brain stimulation in The Virtual Brain (advanced)
- Clinical Applications - Stroke Recovery & Dementia (advanced)
- Evoked Responses in the Visual Cortex (advanced)
- Exploring a model (advanced)
- Hands-On: Modeling stroke brain (advanced)
- Human Brain Project (HBP) TVB-NEST co-simulation (advanced)
- Import Virtual Brain ready data into TVB and create a brain model (advanced)
- Integrated workflows: Image processing pipeline (advanced)
- Modeling brain dynamics in brain tumor patients using The Virtual Brain (advanced)
- Modeling Epilepsy (advanced)
- Modelling Epilepsy with The Virtual Brain (advanced)
- Region simulation tutorial (advanced)
- Resting State Networks (advanced)
- Simulating The Virtual Mouse Brain (TVMB) (advanced)
- Simulating The Virtual Mouse Brain (TVMB) (Copy) (advanced)
- Surface simulation tutorial (advanced)
- Surface-based simulations and deep brain stimulations (advanced)
- The Bayesian Virtual Epileptic Patient (BVEP) (advanced)
- TVB to NEST multi-scale simulation (advanced)
VoluBA
ilastik
- Boundary-based segmentation with Multicut (advanced)
- Carving Workflow (advanced)
- Cell Density Counting Workflow (advanced)
- EBRAINS Atlases - QUINT workflow Tutorial (advanced)
- Object Classification (advanced)
- Pixel Classification workflow (advanced)
- Tracking MaMuT Export (advanced)
- Tracking workflow (advanced)